A bacteriocin discovery pipeline called BOA. Bacteriocin are ribosomal synthesize anti bacterial compounds. BOA provides leads for bacteriocin discovery
2. Antibiotic resistance
WHO (2014): “A problem so serious that it threatens the achievements
of modern medicine... A post-antibiotic era, in which common infections and
minor injuries can kill, far from being an apocalyptic fantasy,
is instead a very real possibility for the 21st century.”
6. The Wide World of Bacteriocins
Antimicrobial Peptides
Nisin A
Microcin B17
Berninamycin A
Microcin J25
Bacteriocin AS-48
Virulence Factors
Streptolysin S
Listeriolysin S
Clostridiolysin S
CylLL + CylLS
Signaling Peptides
RNPP/Rgg
Agr
Gly-Gly
7. Bacteriocins Antibiotics
Synthesis Ribosomal Secondary metabolite
Bioactivity spectra Mostly narrow Mostly broad
Intensity of
bioactivity
Active at nano-to-
micro molar range
Active at micro-to-milli molar range
Proteolytic enzyme
degradability
High Moderate-to-none
Thermal stability High Low
Active pH range Wide Narrow
Possible mechanism
of target cell
developing
resistance
Adaptation
through changes
in cell membrane
composition
Genetically transferable
determinant that inactivates the
active compound
Mode of action Pore formation,
inhibition of cell
wall biosynthesis
Cell membrane or intercellular
targets, inhibition cell wall
biosynthesis
21. So how do we find more
bacteriocins?
Antimicrobial Peptides
Nisin A
Microcin B17
Berninamycin A
Microcin J25
Bacteriocin AS-48
Virulence Factors
Streptolysin S
Listeriolysin S
Clostridiolysin S
CylLL + CylLS
Signaling Peptides
RNPP/Rgg
Agr
Gly-Gly
36. Top 3 Genomes: Different Ecosystems
Streptococcus equi Streptomyces griseus Leifsonia xyli
37. Summing Up
● Annotated genbank files with all predicted bacteriocin
blocks are available
● Need more curated bacteriocin blocks for training
● Explore use of feature vectors with different
combinations / weights of context genes
● Feed into experiments ← → and back
● https://github.com/idoerg/BOA
● Paper & data in production BMC Bioinformatics
● http://arxiv.org/abs/1510.06008
39. Bioinformatics & Computational
Biology PhD Program
● Well-established program, since 2000
● Strengths in: genomics, structural bioinformatics, evolution,
bioengineering
● NSF Training grant in plant phenomics
● $$$ from: Graduate College, Vice Provost Presidential Initiative
Fellowships; Students take part in major plant and
pharmaceutical company internships
● Recent Big Data presidential initiative faculty hires in
metagenomics, phylogenetics, protein function prediction & more.
● Apply by February 15